canns 0.12.7__py3-none-any.whl → 0.13.0__py3-none-any.whl

canns/pipeline/asa/screens.py

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+"""Modal screens for ASA TUI.
+
+This module provides modal overlays for directory selection, help, and error display.
+"""
+
+from pathlib import Path
+
+from textual.app import ComposeResult
+from textual.containers import Container
+from textual.screen import ModalScreen
+from textual.widgets import Button, DirectoryTree, Label, Static
+
+
+class WorkdirScreen(ModalScreen[Path]):
+    """Modal screen for selecting working directory."""
+
+    DEFAULT_CSS = """
+    WorkdirScreen {
+        align: center middle;
+    }
+
+    WorkdirScreen > Container {
+        width: 80;
+        height: 30;
+        border: thick $accent;
+        background: $surface;
+    }
+
+    #workdir-tree {
+        height: 1fr;
+    }
+    """
+
+    def compose(self) -> ComposeResult:
+        with Container():
+            yield Label("Select Working Directory")
+            yield DirectoryTree(Path.home(), id="workdir-tree")
+            with Container(id="button-container"):
+                yield Button("Select", variant="primary", id="select-btn")
+                yield Button("Cancel", id="cancel-btn")
+
+    def on_button_pressed(self, event: Button.Pressed) -> None:
+        if event.button.id == "select-btn":
+            tree = self.query_one("#workdir-tree", DirectoryTree)
+            if tree.cursor_node:
+                selected_path = tree.cursor_node.data.path
+                self.dismiss(selected_path)
+        elif event.button.id == "cancel-btn":
+            self.dismiss(None)
+
+
+class HelpScreen(ModalScreen):
+    """Modal screen showing help and key bindings."""
+
+    DEFAULT_CSS = """
+    HelpScreen {
+        align: center middle;
+    }
+
+    HelpScreen > Container {
+        width: 70;
+        height: 25;
+        border: thick $primary;
+        background: $surface;
+        padding: 2;
+    }
+
+    #help-content {
+        overflow-y: scroll;
+    }
+    """
+
+    HELP_TEXT = """
+ASA TUI - Terminal User Interface for ASA Analysis
+
+KEY BINDINGS:
+  Ctrl-W    Change working directory
+  Ctrl-R    Run analysis
+  F5        Refresh previews
+  ?         Show this help
+  Esc       Quit application
+  Tab       Navigate between panels
+
+ANALYSIS MODULES:
+  TDA           Topological Data Analysis
+  CohoMap       Cohomology Map (requires TDA)
+  PathCompare   Trajectory Comparison (requires CohoMap)
+  CohoSpace     Cohomology Space Visualization (requires CohoMap)
+  FR            Firing Rate Heatmap
+  FRM           Single Neuron Firing Rate Map
+  GridScore     Grid Cell Analysis
+
+WORKFLOW:
+  1. Select working directory (Ctrl-W)
+  2. Choose input mode (ASA or Neuron+Traj)
+  3. Load files
+  4. Configure preprocessing
+  5. Select analysis mode
+  6. Set parameters
+  7. Run analysis (Ctrl-R)
+  8. View results
+
+TERMINAL REQUIREMENTS:
+  Minimum size: 100 cols × 30 rows
+  Recommended: 120 cols × 40 rows
+  Tip: Use smaller font size for better display
+
+  If display is incomplete, try:
+  - Reduce terminal font size
+  - Maximize terminal window
+  - Use fullscreen mode
+
+Press any key to close...
+    """
+
+    def compose(self) -> ComposeResult:
+        with Container():
+            yield Label("Help", id="help-title")
+            yield Static(self.HELP_TEXT, id="help-content")
+            yield Button("Close", variant="primary", id="close-btn")
+
+    def on_button_pressed(self, event: Button.Pressed) -> None:
+        if event.button.id == "close-btn":
+            self.dismiss()
+
+    def on_key(self, event) -> None:
+        self.dismiss()
+
+
+class ErrorScreen(ModalScreen):
+    """Modal screen for displaying errors."""
+
+    DEFAULT_CSS = """
+    ErrorScreen {
+        align: center middle;
+    }
+
+    ErrorScreen > Container {
+        width: 60;
+        height: 20;
+        border: thick $error;
+        background: $surface;
+        padding: 2;
+    }
+
+    #error-message {
+        color: $error;
+        overflow-y: scroll;
+    }
+    """
+
+    def __init__(self, title: str, message: str, **kwargs):
+        super().__init__(**kwargs)
+        self.error_title = title
+        self.error_message = message
+
+    def compose(self) -> ComposeResult:
+        with Container():
+            yield Label(self.error_title, id="error-title")
+            yield Static(self.error_message, id="error-message")
+            yield Button("Close", variant="error", id="close-btn")
+
+    def on_button_pressed(self, event: Button.Pressed) -> None:
+        if event.button.id == "close-btn":
+            self.dismiss()
+
+
+class TerminalSizeWarning(ModalScreen):
+    """Warning screen for insufficient terminal size."""
+
+    DEFAULT_CSS = """
+    TerminalSizeWarning {
+        align: center middle;
+    }
+
+    TerminalSizeWarning > Container {
+        width: 50;
+        height: 15;
+        border: thick $warning;
+        background: $surface;
+        padding: 2;
+    }
+
+    #warning-message {
+        color: $warning;
+        text-align: center;
+    }
+    """
+
+    def __init__(self, current_width: int, current_height: int, **kwargs):
+        super().__init__(**kwargs)
+        self.current_width = current_width
+        self.current_height = current_height
+
+    def compose(self) -> ComposeResult:
+        with Container():
+            yield Label("⚠ Terminal Size Warning", id="warning-title")
+            yield Static(
+                f"Current terminal size: {self.current_width} cols × {self.current_height} rows\n\n"
+                f"Recommended minimum:\n"
+                f"• Width: 100 columns (recommended 120+)\n"
+                f"• Height: 30 rows (recommended 40+)\n\n"
+                f"Please resize terminal or reduce font size.\n"
+                f"Press Esc to continue (may not display properly)",
+                id="warning-message",
+            )
+            yield Button("Continue", variant="warning", id="continue-btn")
+
+    def on_button_pressed(self, event: Button.Pressed) -> None:
+        if event.button.id == "continue-btn":
+            self.dismiss()
+
+    def on_key(self, event) -> None:
+        if event.key == "escape":
+            self.dismiss()

canns/pipeline/asa/state.py

@@ -0,0 +1,248 @@
+"""State management for ASA TUI.
+
+This module provides centralized workflow state management with workdir-centric design.
+All file paths are stored relative to the working directory for portability.
+"""
+
+from dataclasses import dataclass, field
+from pathlib import Path
+from typing import Any
+
+
+@dataclass
+class WorkflowState:
+    """Centralized state for ASA analysis workflow.
+
+    All file paths are relative to workdir for portability.
+    """
+
+    # Core paths
+    workdir: Path = field(default_factory=lambda: Path("."))
+
+    # Input configuration
+    input_mode: str = "asa"  # "asa" | "neuron_traj" | "batch"
+    preset: str = "grid"  # "grid" | "hd" | "none"
+
+    # File paths (relative to workdir)
+    asa_file: Path | None = None
+    neuron_file: Path | None = None
+    traj_file: Path | None = None
+
+    # Preprocessing
+    preprocess_method: str = "none"  # "none" | "embed_spike_trains"
+    preprocess_params: dict[str, Any] = field(default_factory=dict)
+
+    # Analysis configuration
+    analysis_mode: str = (
+        "tda"  # "tda" | "cohomap" | "pathcompare" | "cohospace" | "fr" | "frm" | "gridscore"
+    )
+    analysis_params: dict[str, Any] = field(default_factory=dict)
+
+    # Results
+    artifacts: dict[str, Path] = field(default_factory=dict)
+
+    # Runtime state
+    is_running: bool = False
+    current_stage: str = ""
+
+
+def relative_path(state: WorkflowState, path: Path) -> Path:
+    """Convert absolute path to workdir-relative path.
+
+    Args:
+        state: Current workflow state
+        path: Absolute path to convert
+
+    Returns:
+        Path relative to workdir
+    """
+    try:
+        return path.relative_to(state.workdir)
+    except ValueError:
+        # Path is not relative to workdir, return as-is
+        return path
+
+
+def resolve_path(state: WorkflowState, path: Path | None) -> Path | None:
+    """Convert relative path to absolute path.
+
+    Args:
+        state: Current workflow state
+        path: Relative path to convert
+
+    Returns:
+        Absolute path or None if path is None
+    """
+    if path is None:
+        return None
+
+    if path.is_absolute():
+        return path
+
+    return state.workdir / path
+
+
+def validate_files(state: WorkflowState) -> tuple[bool, str]:
+    """Check if required files exist.
+
+    Args:
+        state: Current workflow state
+
+    Returns:
+        Tuple of (is_valid, error_message)
+    """
+    if state.input_mode == "asa":
+        if state.asa_file is None:
+            return False, "ASA file not selected"
+
+        asa_path = resolve_path(state, state.asa_file)
+        if not asa_path.exists():
+            return False, f"ASA file not found: {asa_path}"
+
+        # Validate .npz structure
+        try:
+            import numpy as np
+
+            data = np.load(asa_path, allow_pickle=True)
+            required_keys = ["spike", "t"]
+            missing = [k for k in required_keys if k not in data.files]
+            if missing:
+                return False, f"ASA file missing required keys: {missing}"
+        except Exception as e:
+            return False, f"Failed to load ASA file: {e}"
+
+    elif state.input_mode == "neuron_traj":
+        if state.neuron_file is None:
+            return False, "Neuron file not selected"
+        if state.traj_file is None:
+            return False, "Trajectory file not selected"
+
+        neuron_path = resolve_path(state, state.neuron_file)
+        traj_path = resolve_path(state, state.traj_file)
+
+        if not neuron_path.exists():
+            return False, f"Neuron file not found: {neuron_path}"
+        if not traj_path.exists():
+            return False, f"Trajectory file not found: {traj_path}"
+
+    return True, ""
+
+
+def get_preset_params(preset: str) -> dict[str, Any]:
+    """Load preset configurations for analysis.
+
+    Args:
+        preset: Preset name ("grid", "hd", or "none")
+
+    Returns:
+        Dictionary of preset parameters
+    """
+    if preset == "grid":
+        return {
+            "preprocess": {
+                "method": "embed_spike_trains",
+                "dt": 0.02,
+                "sigma": 0.1,
+                "speed_filter": False,
+                "min_speed": 2.5,
+            },
+            "tda": {
+                "dim": 6,
+                "num_times": 5,
+                "active_times": 15000,
+                "k": 1000,
+                "n_points": 1200,
+                "metric": "cosine",
+                "nbs": 800,
+                "maxdim": 1,
+                "coeff": 47,
+                "do_shuffle": False,
+                "num_shuffles": 1000,
+            },
+            "gridscore": {
+                "annulus_inner": 0.3,
+                "annulus_outer": 0.7,
+                "bin_size": 2.5,
+                "smooth_sigma": 2.0,
+            },
+        }
+    elif preset == "hd":
+        return {
+            "preprocess": {
+                "method": "embed_spike_trains",
+                "dt": 0.02,
+                "sigma": 0.1,
+                "speed_filter": False,
+                "min_speed": 2.5,
+            },
+            "tda": {
+                "dim": 4,
+                "num_times": 5,
+                "active_times": 15000,
+                "k": 800,
+                "n_points": 1000,
+                "metric": "cosine",
+                "nbs": 600,
+                "maxdim": 1,
+                "coeff": 47,
+                "do_shuffle": False,
+                "num_shuffles": 1000,
+            },
+        }
+    else:  # "none"
+        return {}
+
+
+def check_cached_artifacts(state: WorkflowState, stage: str) -> bool:
+    """Check if stage artifacts exist and are valid.
+
+    Args:
+        state: Current workflow state
+        stage: Analysis stage name
+
+    Returns:
+        True if cached artifacts exist and are valid
+    """
+    stage_dir = state.workdir / stage
+    if not stage_dir.exists():
+        return False
+
+    # Define required files for each stage
+    stage_artifacts = {
+        "TDA": ["barcode.png", "persistence.npz"],
+        "CohoMap": ["decoding.npz", "cohomap.png"],
+        "PathCompare": ["path_compare.png"],
+        "CohoSpace": ["cohospace_trajectory.png"],
+        "FR": ["fr_heatmap.png"],
+        "FRM": [],  # Dynamic based on neuron_id
+        "GridScore": ["gridscore_distribution.png", "gridscore.npz"],
+    }
+
+    required_files = stage_artifacts.get(stage, [])
+    return all((stage_dir / f).exists() for f in required_files)
+
+
+def load_cached_result(state: WorkflowState, stage: str) -> dict[str, Any]:
+    """Load cached results from previous run.
+
+    Args:
+        state: Current workflow state
+        stage: Analysis stage name
+
+    Returns:
+        Dictionary of cached data
+    """
+    import numpy as np
+
+    stage_dir = state.workdir / stage
+    result = {}
+
+    # Load .npz files
+    for npz_file in stage_dir.glob("*.npz"):
+        try:
+            data = np.load(npz_file, allow_pickle=True)
+            result[npz_file.stem] = dict(data)
+        except Exception:
+            pass
+
+    return result

canns/pipeline/asa/styles.tcss

@@ -0,0 +1,221 @@
+/* ASA TUI Styles */
+
+/* Hidden class */
+.hidden {
+    display: none;
+}
+
+/* Main layout - three columns */
+#main-container {
+    layout: horizontal;
+    height: 100%;
+}
+
+/* Left panel - narrow action panel */
+#left-panel {
+    width: 22;
+    min-width: 20;
+    max-width: 26;
+    height: 100%;  /* CRITICAL: Fill parent height */
+    border-right: solid $primary;
+    padding: 1;
+}
+
+/* Scrollable controls area - fill remaining height to enable scrolling */
+#controls-scroll {
+    height: 1fr;
+    overflow-y: auto;
+    scrollbar-size-vertical: 1;
+    min-width: 100%;
+    padding-bottom: 2;
+}
+
+/* Child containers expand naturally to allow scrolling */
+#preprocess-controls,
+#analysis-controls {
+    height: auto !important;
+    width: 100%;
+}
+
+/* Middle panel - parameters + file browser */
+#middle-panel {
+    layout: horizontal;
+    width: 0.5fr;
+    min-width: 30;
+    border-right: solid $primary;
+    padding: 0;
+}
+
+#params-panel {
+    width: 0.7fr;
+    padding: 1;
+    border-right: solid $secondary;
+    height: 100%;
+}
+
+#params-header {
+    background: $boost;
+    padding: 1;
+    margin-bottom: 1;
+    text-style: bold;
+}
+
+#file-tree-panel {
+    width: 0.7fr;
+    padding: 1;
+    height: 100%;
+}
+
+#files-header {
+    background: $boost;
+    padding: 1;
+    margin-bottom: 1;
+    text-style: bold;
+}
+
+#right-panel {
+    width: 1.5fr;
+    padding: 1;
+    height: 100%;
+}
+
+/* Results tabs take 75% of right panel height */
+#results-tabs {
+    height: 5fr;
+}
+
+/* Log viewer at bottom - 25% of right panel height */
+#log-viewer {
+    height: 1fr;
+    border: solid $primary;
+    padding: 1;
+}
+
+/* Workdir label */
+#workdir-label {
+    background: $boost;
+    padding: 1;
+    margin-bottom: 1;
+}
+
+/* Parameter groups */
+ParamGroup {
+    border: round $secondary;
+    padding: 1;
+    padding-bottom: 1;
+    margin: 1 0;
+    height: auto;
+    width: 100%;
+    min-height: 10;
+}
+
+.param-group-title {
+    text-style: bold;
+    color: $accent;
+    dock: top;
+}
+
+/* Embedding parameters container */
+#emb-params {
+    margin-top: 1;
+    margin-bottom: 1;
+    height: auto !important;
+}
+
+#emb-params Label {
+    margin-top: 1;
+}
+
+#emb-params Input {
+    margin-bottom: 1;
+}
+
+#emb-params Checkbox {
+    margin: 1 0;  /* Changed from 0.5 to 1 */
+}
+
+/* Buttons */
+Button {
+    margin: 1 0;
+}
+
+#actions-bar {
+    width: 100%;
+    margin: 0 0 1 0;
+}
+
+#actions-bar Button {
+    width: 100%;
+    margin: 0 0 1 0;
+}
+
+#run-btn {
+    width: 100%;
+    margin-top: 2;
+}
+
+/* Progress bar */
+#progress-bar {
+    margin: 1 0;
+}
+
+#run-status {
+    margin-top: 1;
+}
+
+/* Image preview - allow more space */
+ImagePreview {
+    height: 1fr;
+    min-height: 20;
+    border: solid $accent;
+    padding: 1;
+}
+
+#preview-path {
+    color: $text-muted;
+    margin-bottom: 1;
+}
+
+#preview-path-input {
+    margin-bottom: 1;
+}
+
+/* File tree - compact for small terminals, now full height */
+#file-tree {
+    height: 1fr;  /* Fill available space */
+    border: solid $secondary;
+}
+
+/* Status indicators */
+.running {
+    background: $warning;
+}
+
+.success {
+    background: $success;
+}
+
+.error {
+    background: $error;
+}
+
+/* Tab content */
+TabbedContent {
+    height: 1fr;
+}
+
+TabPane {
+    padding: 1;
+    height: 100%;
+}
+
+TabbedContent > ContentSwitcher {
+    height: 1fr;
+}
+
+/* Result status */
+#result-status {
+    margin-top: 2;
+    padding: 1;
+    border: solid $primary;
+}